From ccp4null@dl.ac.uk Wed Dec 7 11:48:26 2005 Date: Wed, 11 May 2005 11:40:07 +0100 From: OnLineHelpForm Reply-To: zhenbo@chem.gla.ac.uk To: ccp4@ccp4.ac.uk Subject: [ccp4]: problems with - areaimol I am using ccp4 version release-5_0. I am using ccp4i. I am using the macos operating system. My compiler is: native I installed using compilesource The problem is as follows: Hi there, I try to run this program but failed with this message: MODE set to NOHOH No symmetry related atoms will be generated ERROR: Dimension of NET too small in program. Need: 12362350 Currently: 6000000 AREAIMOL: Parameter MAXNET too small Times: User: 0.5s System: 0.1s Elapsed: 0:01 my structure is quite big, like 600 kD. so is there anything I can do about it? Thanks! I have done the following patches: No - but I will go back and check them now! I am having a problem with a program. The program is areaimol. Thanks in advance, Zhenbo cao, zhenbo@chem.gla.ac.uk **** start program.log **** #CCP4I VERSION CCP4Interface 1.3.20 #CCP4I SCRIPT LOG areaimol #CCP4I DATE 11 May 2005 10:06:42 #CCP4I USER zhenbo #CCP4I PROJECT mr #CCP4I JOB_ID 54 #CCP4I SCRATCH /tmp/zhenbo #CCP4I HOSTNAME zhenbo-caos-computer.local #CCP4I PID 420

AREAIMOL

 
 
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 ### CCP4 5.0: AREAIMOL           version 5.0       : 30/01/04##
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 User: zhenbo  Run date: 11/ 5/2005 Run time: 10:06:42 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.





Contents






Command Input



   Main Keywords

DIFFMODE   
MODE 
SMODE 
SYMMETRY  
TRANS


   Secondary Keywords

ATOM   
EXCLUDE 
MATCHUP 
PNTDEN 
PROBE  


   Auxiliary Keywords

VERBOSE  
OUTPUT  
END

 NOTE: this is an updated version of AREAIMOL which also
 includes the functions of the old RESAREA, WATERAREA and
 DIFFAREA programs

 See program documentation for details.


 Data line--- DIFFMODE OFF
 Data line--- MODE     NOHOH
 Data line--- SMODE OFF
 Data line--- PNTDEN 10
 Data line--- PROBE 1.4
 Data line--- OUTPUT
 Data line--- END



Mode


 DIFFMODE OFF: single area calculation

 MODE NOHOH - Residue types HOH and WAT will be ignored

 SMODE OFF - symmetry-related atoms will not be generated


 Solvent/probe radius set to   1.40 A

 Number of points/area used in AREA calculation set to 
 10.00 per angstrom squared


 Areas will be written to PDB-style output file
 (area/area difference written to B-factor column)


 Search for isolated areas of surface will be performed
 This will identify unconnected surface areas, including cavities
 inside the molecule


  Logical name: XYZIN  File name: /Users/zhenbo/xtal_data/c168s/refine/1ring.pdb
  PDB file is being opened on unit 1 for INPUT.

  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE


             RF                                  RO

    0.003  -0.000   0.001  -0.000      300.995   0.000 -48.086   0.000
   -0.000   0.012  -0.000   0.000        0.000  80.679   0.000   0.000
    0.000  -0.000   0.009  -0.000        0.000   0.000 114.617   0.000
   -0.000   0.000  -0.000   1.000        0.000   0.000   0.000   1.000


  $WARNING: NO SCALE CARDS READ$



Data From Input Coordinate File



 READING IN ATOM DATA FROM INPUT COORDINATE FILE


 Read in 18432 atoms from pdb file of which there were:

   11796 atoms of type  C (number  6)
    3108 atoms of type  N (number  7)
    3492 atoms of type  O (number  8)
      36 atoms of type  S (number 16)

 All atoms were identified


 One or more atoms had occupancy < 1.0 in input file.





Total Area Calculation



 ===================== STARTING AREA CALCULATION =====================

 MODE set to NOHOH

 No symmetry related atoms will be generated
 ERROR: Dimension of NET too small in program. Need: 
  12362350  Currently:    6000000

 AREAIMOL:  Parameter MAXNET too small
Times: User:       0.5s System:    0.1s Elapsed:     0:01
*************************************************************************** * Information from CCP4Interface script *************************************************************************** The program run with command: areaimol XYZIN /Users/zhenbo/xtal_data/c168s/refine/1ring.pdb XYZOUT /Users/zhenbo/xtal_data/c168s/ccp4/1ring_areaimol1.pdb has failed with error message AREAIMOL: Parameter MAXNET too small *************************************************************************** #CCP4I TERMINATION STATUS 0 " AREAIMOL: Parameter MAXNET too small" #CCP4I TERMINATION TIME 11 May 2005 10:06:43 #CCP4I MESSAGE Task failed **** end program.log ****